Sidebar
Sample summary
Input data: infant stools
- n samples = 341
- n features: 2387
- mean read count: 10^{6}, s.d. = 0
Alpha diversity
Column
Seroconversion
Blue = seroconversion+, Orange = seroconversion-.
Seroconverion - N by country
IND IND (neo+) IND (neo-) MLW
0 204 104 99 46
1 78 45 33 10Mean + s.d.
seroconv Observed.mean Observed.sd Observed.country
1 0 1471.68 194.31 IND
2 1 1401.24 243.34 IND
3 0 1489.88 165.36 IND (neo+)
4 1 1419.29 224.65 IND (neo+)
5 0 1451.28 220.31 IND (neo-)
6 1 1376.64 268.35 IND (neo-)
7 0 1452.96 172.13 MLW
8 1 1378.2 241.94 MLWSeroconverion - P values
[,1]
IND 0.022965
MLW 0.404078
IND_exposed 0.014502
IND_nonexposed 0.039949RV-IgA
Correlation heatmap
Collated results
rho p n
IND -0.0229 0.701882 282
IND (neo+) 0.0112 0.891822 149
IND (neo-) -0.0844 0.335820 132
MLW -0.2474 0.066025 56Dose 1 shedding
Blue = shed+, Orange = shed-.
Dose 1 shedding - N by country
IND IND (neo+) IND (neo-) MLW
0 207 122 83 26
1 74 25 49 21Mean + s.d.
dose1_shedding Observed.mean Observed.sd Observed.country
1 0 1458.44 202.03 IND
2 1 1439.91 231.84 IND
3 0 1469.04 190.09 IND (neo+)
4 1 1482.64 164.6 IND (neo+)
5 0 1441.19 220.25 IND (neo-)
6 1 1418.1 258.38 IND (neo-)
7 0 1466.35 162.23 MLW
8 1 1422.29 201.26 MLWDose 1 shedding - P values
[,1]
IND 0.648492
MLW 0.401555
IND_exposed 0.824418
IND_nonexposed 0.582478Beta diversity
Column
Seroconversion
Summary
R2 p n country full outcome
IND_BS3 1.257757 0.021 282 IND 1 seroconversion
INDexp_BS3 1.869036 0.035 149 IND (neo+) 0 seroconversion
INDunexp_BS3 1.282014 0.154 132 IND (neo-) 0 seroconversion
MLW_BS3 1.929854 0.338 56 MLW 1 seroconversionSummary plot
RV-IgA
Summary
R2 p n country full outcome
IND_BS3 0.2184339 0.639 282 IND 1 RV-IgA (post-ORV)
INDexp_BS3 0.7045396 0.317 149 IND (neo+) 0 RV-IgA (post-ORV)
INDunexp_BS3 1.5668623 0.105 132 IND (neo-) 0 RV-IgA (post-ORV)
MLW_BS3 3.2719980 0.097 56 MLW 1 RV-IgA (post-ORV)Summary plot
Dose 1 shedding
Summary
R2 p n country full outcome
IND_BS3 0.1975244 0.657 281 IND 1 dose 1 shedding
INDexp_BS3 0.1787830 0.983 147 IND (neo+) 0 dose 1 shedding
INDunexp_BS3 0.5350290 0.492 132 IND (neo-) 0 dose 1 shedding
MLW_BS3 1.3106750 0.716 47 MLW 1 dose 1 sheddingSummary plot
Random Forests/MaAsLin2
Column
Seroconversion
Summary plot
Differential features - FDR p <0.2
country n_tested_fisher n_signif_fisher n_tested_lr n_signif_lr
1 MLW 1375 0 1375 0
2 IND (neo-) 1460 0 1460 0
3 IND (neo+) 1266 0 1266 0
4 IND 1368 0 1368 0
n_tested_maaslin n_signif_maaslin
1 2010 0
2 2033 0
3 1990 0
4 1997 0
Summary of prevalence difference distribution
Proportion of features more prevalent in non-responders vs responders
country n_neg n_equal n_pos total proportion_neg
1 IND 1155 7 206 1368 84.4%
2 IND (neo+) 992 8 266 1266 78.4%
3 IND (neo-) 1125 46 289 1460 77.1%
4 MLW 974 6 395 1375 70.8%n = prevalence difference <0 (vs >=0).
P values (Wilcoxon test, mean of difference distribution = 0)
[,1]
IND 1.278089e-156
MLW 2.218671e-58
IND_exposed 2.008546e-115
IND_nonexposed 2.828480e-120Summary of adundance difference distribution
P values (Wilcoxon test, mean of difference distribution = 0)
[,1]
IND 1.066623e-70
MLW 5.329477e-44
IND_exposed 3.269710e-89
IND_nonexposed 9.008120e-24Proportion of features more abundant in non-responders vs responders
country n_neg n_equal n_pos total proportion_neg
1 IND 1316 0 681 1997 65.9%
2 IND (neo+) 1350 0 640 1990 67.8%
3 IND (neo-) 1250 0 783 2033 61.5%
4 MLW 1275 0 735 2010 63.4%Summary of MaAsLin2 associations
subset N_features FDR p<0.2 unadjusted FDR p<0.2 adjusted
1 IND 1997 (681 +/1316 -) 0 (0 +/0 -) 0 (0 +/0 -)
2 IND (neo+) 1990 (640 +/1350 -) 0 (0 +/0 -) 0 (0 +/0 -)
3 IND (neo-) 2033 (783 +/1250 -) 0 (0 +/0 -) 0 (0 +/0 -)
4 MLW 2010 (735 +/1275 -) 0 (0 +/0 -) 0 (0 +/0 -)Spearman’s rho matrix of statistical test p values - India
#### Rho values
Fisher p LR p LR (adj) p Wilcox p
Fisher p 1.0000000 0.9844538 0.9574237 0.7718970
LR p 0.9844538 1.0000000 0.9716970 0.7583236
LR (adj) p 0.9574237 0.9716970 1.0000000 0.7459578
Wilcox p 0.7718970 0.7583236 0.7459578 1.0000000
Maaslin p 0.6026035 0.5908554 0.5935672 0.8683797
Maaslin (adj) p 0.5710366 0.5580255 0.5829360 0.8310340
RF rank 0.1559357 0.1598539 0.1290991 0.1591355
Inv. abs. Maaslin coef. (adj) 0.5265761 0.5312382 0.5297777 0.7544746
Inv. abs. Prev. diff. 0.8866968 0.8875929 0.8295230 0.6305928
Inv. abs. ean abund. diff. 0.3490231 0.3579612 0.3462378 0.5436753
Maaslin p Maaslin (adj) p RF rank
Fisher p 0.6026035 0.5710366 0.1559357
LR p 0.5908554 0.5580255 0.1598539
LR (adj) p 0.5935672 0.5829360 0.1290991
Wilcox p 0.8683797 0.8310340 0.1591355
Maaslin p 1.0000000 0.9626950 0.1419771
Maaslin (adj) p 0.9626950 1.0000000 0.1535183
RF rank 0.1419771 0.1535183 1.0000000
Inv. abs. Maaslin coef. (adj) 0.7879172 0.7603945 0.3037155
Inv. abs. Prev. diff. 0.4500090 0.4186107 0.2240846
Inv. abs. ean abund. diff. 0.5995824 0.5250607 0.2547454
Inv. abs. Maaslin coef. (adj)
Fisher p 0.5265761
LR p 0.5312382
LR (adj) p 0.5297777
Wilcox p 0.7544746
Maaslin p 0.7879172
Maaslin (adj) p 0.7603945
RF rank 0.3037155
Inv. abs. Maaslin coef. (adj) 1.0000000
Inv. abs. Prev. diff. 0.3480356
Inv. abs. ean abund. diff. 0.8789450
Inv. abs. Prev. diff. Inv. abs. ean abund. diff.
Fisher p 0.8866968 0.3490231
LR p 0.8875929 0.3579612
LR (adj) p 0.8295230 0.3462378
Wilcox p 0.6305928 0.5436753
Maaslin p 0.4500090 0.5995824
Maaslin (adj) p 0.4186107 0.5250607
RF rank 0.2240846 0.2547454
Inv. abs. Maaslin coef. (adj) 0.3480356 0.8789450
Inv. abs. Prev. diff. 1.0000000 0.1676328
Inv. abs. ean abund. diff. 0.1676328 1.0000000
N features with full data across tests: 1368
Spearman’s rho matrix of statistical test p values - India (neo+)
#### Rho values
Fisher p LR p LR (adj) p Wilcox p
Fisher p 1.0000000 0.9637773 0.9105098 0.8221429
LR p 0.9637773 1.0000000 0.9449763 0.8041502
LR (adj) p 0.9105098 0.9449763 1.0000000 0.7605289
Wilcox p 0.8221429 0.8041502 0.7605289 1.0000000
Maaslin p 0.6633433 0.6451387 0.6129365 0.8816638
Maaslin (adj) p 0.6398416 0.6210334 0.6290591 0.8530445
RF rank 0.1980933 0.2023137 0.2195135 0.2442057
Inv. abs. Maaslin coef. (adj) 0.6029447 0.6010415 0.5785742 0.7748324
Inv. abs. prev. diff. 0.9141777 0.9102090 0.8497862 0.6965717
Inv. abs. mean abund. diff. 0.4389689 0.4405678 0.4024563 0.5735290
Maaslin p Maaslin (adj) p RF rank
Fisher p 0.6633433 0.6398416 0.1980933
LR p 0.6451387 0.6210334 0.2023137
LR (adj) p 0.6129365 0.6290591 0.2195135
Wilcox p 0.8816638 0.8530445 0.2442057
Maaslin p 1.0000000 0.9470219 0.2031067
Maaslin (adj) p 0.9470219 1.0000000 0.2221453
RF rank 0.2031067 0.2221453 1.0000000
Inv. abs. Maaslin coef. (adj) 0.8074664 0.8442730 0.3114884
Inv. abs. prev. diff. 0.5230474 0.4883343 0.2483094
Inv. abs. mean abund. diff. 0.6250153 0.5939432 0.2206224
Inv. abs. Maaslin coef. (adj)
Fisher p 0.6029447
LR p 0.6010415
LR (adj) p 0.5785742
Wilcox p 0.7748324
Maaslin p 0.8074664
Maaslin (adj) p 0.8442730
RF rank 0.3114884
Inv. abs. Maaslin coef. (adj) 1.0000000
Inv. abs. prev. diff. 0.4460297
Inv. abs. mean abund. diff. 0.8629805
Inv. abs. prev. diff. Inv. abs. mean abund. diff.
Fisher p 0.9141777 0.4389689
LR p 0.9102090 0.4405678
LR (adj) p 0.8497862 0.4024563
Wilcox p 0.6965717 0.5735290
Maaslin p 0.5230474 0.6250153
Maaslin (adj) p 0.4883343 0.5939432
RF rank 0.2483094 0.2206224
Inv. abs. Maaslin coef. (adj) 0.4460297 0.8629805
Inv. abs. prev. diff. 1.0000000 0.2819992
Inv. abs. mean abund. diff. 0.2819992 1.0000000
N features with full data across tests: 1266
Spearman’s rho matrix of statistical test p values - India (neo-)
#### Rho values
Fisher p LR p LR (adj) p Wilcox p
Fisher p 1.0000000 0.8510421 0.7449071 0.5827697
LR p 0.8510421 1.0000000 0.8839418 0.4509089
LR (adj) p 0.7449071 0.8839418 1.0000000 0.2902918
Wilcox p 0.5827697 0.4509089 0.2902918 1.0000000
Maaslin p 0.3388825 0.2135994 0.1006075 0.7717718
Maaslin (adj) p 0.3466042 0.2218835 0.1579571 0.7308316
RF rank 0.2190930 0.3130324 0.2967191 0.2005985
Inv. abs. Maaslin coef. (adj) 0.2678914 0.3050515 0.3802081 0.4159349
Inv. abs. prev. diff. 0.9018392 0.8519589 0.6872441 0.5566433
Inv. abs. mean abund. diff. 0.1574034 0.2189754 0.2734100 0.2084495
Maaslin p Maaslin (adj) p RF rank
Fisher p 0.3388825 0.3466042 0.2190930
LR p 0.2135994 0.2218835 0.3130324
LR (adj) p 0.1006075 0.1579571 0.2967191
Wilcox p 0.7717718 0.7308316 0.2005985
Maaslin p 1.0000000 0.9121438 0.1535434
Maaslin (adj) p 0.9121438 1.0000000 0.1426679
RF rank 0.1535434 0.1426679 1.0000000
Inv. abs. Maaslin coef. (adj) 0.4847625 0.5996550 0.4297989
Inv. abs. prev. diff. 0.2876163 0.2675565 0.2737840
Inv. abs. mean abund. diff. 0.2822895 0.2931064 0.5040995
Inv. abs. Maaslin coef. (adj)
Fisher p 0.2678914
LR p 0.3050515
LR (adj) p 0.3802081
Wilcox p 0.4159349
Maaslin p 0.4847625
Maaslin (adj) p 0.5996550
RF rank 0.4297989
Inv. abs. Maaslin coef. (adj) 1.0000000
Inv. abs. prev. diff. 0.1894932
Inv. abs. mean abund. diff. 0.7634261
Inv. abs. prev. diff. Inv. abs. mean abund. diff.
Fisher p 0.90183921 0.15740341
LR p 0.85195892 0.21897545
LR (adj) p 0.68724406 0.27340996
Wilcox p 0.55664335 0.20844951
Maaslin p 0.28761631 0.28228948
Maaslin (adj) p 0.26755652 0.29310635
RF rank 0.27378399 0.50409952
Inv. abs. Maaslin coef. (adj) 0.18949318 0.76342609
Inv. abs. prev. diff. 1.00000000 0.09798481
Inv. abs. mean abund. diff. 0.09798481 1.00000000
N features with full data across tests: 1460
Spearman’s rho matrix of statistical test p values - Malawi
#### Rho values
Fisher p LR p LR (adj) p Wilcox p
Fisher p 1.0000000 0.59721990 0.53774451 0.47185737
LR p 0.5972199 1.00000000 0.93288129 0.22786682
LR (adj) p 0.5377445 0.93288129 1.00000000 0.18203766
Wilcox p 0.4718574 0.22786682 0.18203766 1.00000000
Maaslin p 0.2562869 0.01816358 0.01347839 0.71224601
Maaslin (adj) p 0.2662356 0.02658952 0.02788535 0.65889248
RF rank 0.2142260 0.29817067 0.27072356 0.15950897
Inv. abs. maaslin coef. (adj) 0.3583978 0.25883700 0.23956596 0.32693401
Inv. abs. prev. diff. 0.7704952 0.61164179 0.54479285 0.56229462
Inv. abs. mean abund. diff. 0.2147074 0.18891723 0.17914225 0.07707084
Maaslin p Maaslin (adj) p RF rank
Fisher p 0.25628690 0.26623558 0.21422602
LR p 0.01816358 0.02658952 0.29817067
LR (adj) p 0.01347839 0.02788535 0.27072356
Wilcox p 0.71224601 0.65889248 0.15950897
Maaslin p 1.00000000 0.92954620 0.07089077
Maaslin (adj) p 0.92954620 1.00000000 0.08785871
RF rank 0.07089077 0.08785871 1.00000000
Inv. abs. maaslin coef. (adj) 0.52693580 0.62413904 0.46739949
Inv. abs. prev. diff. 0.27311762 0.24515284 0.21454952
Inv. abs. mean abund. diff. 0.26369062 0.28905627 0.48694201
Inv. abs. maaslin coef. (adj)
Fisher p 0.3583978
LR p 0.2588370
LR (adj) p 0.2395660
Wilcox p 0.3269340
Maaslin p 0.5269358
Maaslin (adj) p 0.6241390
RF rank 0.4673995
Inv. abs. maaslin coef. (adj) 1.0000000
Inv. abs. prev. diff. 0.2246508
Inv. abs. mean abund. diff. 0.7711916
Inv. abs. prev. diff. Inv. abs. mean abund. diff.
Fisher p 0.77049521 0.21470738
LR p 0.61164179 0.18891723
LR (adj) p 0.54479285 0.17914225
Wilcox p 0.56229462 0.07707084
Maaslin p 0.27311762 0.26369062
Maaslin (adj) p 0.24515284 0.28905627
RF rank 0.21454952 0.48694201
Inv. abs. maaslin coef. (adj) 0.22465076 0.77119165
Inv. abs. prev. diff. 1.00000000 0.09143309
Inv. abs. mean abund. diff. 0.09143309 1.00000000
N features with full data across tests: 1375
RV-IgA
Summary plot
Differential features - p <0.2
country n_tested_wilcox n_signif_wilcox n_tested_lr n_signif_lr
1 MLW 1247 0 1247 0
2 IND (neo-) 1274 0 1274 400
3 IND (neo+) 1172 0 1172 0
4 IND 1228 0 1228 0
n_tested_maaslin n_signif_maaslin
1 1970 0
2 1954 0
3 1964 0
4 1956 0
Summary of GMRs
Proportion of features negatively vs positively correlated with RV-IgA
country n_neg n_equal n_pos total proportion_neg
1 IND 561 0 667 1228 45.7%
2 IND (neo+) 416 0 756 1172 35.5%
3 IND (neo-) 1024 0 250 1274 80.4%
4 MLW 973 0 274 1247 78%n = GM ratio <1 (vs >=1).
P values (Wilcoxon test, mean of difference distribution = 1)
[,1]
IND 3.171286e-06
MLW 1.490319e-76
IND_exposed 1.339595e-40
IND_nonexposed 4.547007e-96Summary of adundance difference distribution
P values (Wilcoxon test, mean of difference distribution = 0)
[,1]
IND 8.308490e-01
MLW 1.609518e-11
IND_exposed 3.630871e-10
IND_nonexposed 2.298759e-44Proportion of features negatively vs positively correlated with RV-IgA
country n_neg n_equal n_pos total proportion_neg
1 IND 955 0 1001 1956 48.8%
2 IND (neo+) 839 0 1125 1964 42.7%
3 IND (neo-) 1233 0 721 1954 63.1%
4 MLW 1111 0 859 1970 56.4%Summary of MaAsLin2 associations
subset N_features FDR p<0.2 unadjusted FDR p<0.2 adjusted
1 IND 1956 (1001 +/955 -) 0 (0 +/0 -) 0 (0 +/0 -)
2 IND (neo+) 1964 (1125 +/839 -) 0 (0 +/0 -) 0 (0 +/0 -)
3 IND (neo-) 1954 (721 +/1233 -) 0 (0 +/0 -) 0 (0 +/0 -)
4 MLW 1970 (859 +/1111 -) 0 (0 +/0 -) 0 (0 +/0 -)Spearman’s rho matrix of statistical test p values - India
#### Rho values
Spearman p LR p LR (adj) p Wilcox p
Spearman p 1.00000000 0.08675909 0.07229609 0.52618387
LR p 0.08675909 1.00000000 0.91439954 0.07584457
LR (adj) p 0.07229609 0.91439954 1.00000000 0.03184581
Wilcox p 0.52618387 0.07584457 0.03184581 1.00000000
Maaslin p 0.75111533 0.10166561 0.11224929 0.26559176
Maaslin (adj) p 0.51465286 0.03479046 0.10712021 0.23982589
RF rank 0.13945482 0.14413599 0.13654507 0.02132497
Inv. abs. maaslin coef. (adj) 0.28596906 0.05687729 0.12282509 0.05129690
Inv. abs. GMR-1 0.43196854 0.21226510 0.16196086 0.90906486
Maaslin p Maaslin (adj) p RF rank
Spearman p 0.7511153 0.51465286 0.13945482
LR p 0.1016656 0.03479046 0.14413599
LR (adj) p 0.1122493 0.10712021 0.13654507
Wilcox p 0.2655918 0.23982589 0.02132497
Maaslin p 1.0000000 0.69446300 0.15861409
Maaslin (adj) p 0.6944630 1.00000000 0.07891673
RF rank 0.1586141 0.07891673 1.00000000
Inv. abs. maaslin coef. (adj) 0.4364218 0.74508187 0.17807771
Inv. abs. GMR-1 0.2099464 0.15795986 0.05726359
Inv. abs. maaslin coef. (adj) Inv. abs. GMR-1
Spearman p 0.28596906 0.43196854
LR p 0.05687729 0.21226510
LR (adj) p 0.12282509 0.16196086
Wilcox p 0.05129690 0.90906486
Maaslin p 0.43642180 0.20994642
Maaslin (adj) p 0.74508187 0.15795986
RF rank 0.17807771 0.05726359
Inv. abs. maaslin coef. (adj) 1.00000000 0.01741027
Inv. abs. GMR-1 0.01741027 1.00000000
N features with full data across tests: 1228
Spearman’s rho matrix of statistical test p values - India (neo+)
#### Rho values
Spearman p LR p LR (adj) p Wilcox p
Spearman p 1.0000000 0.35893864 0.2454261 0.53558708
LR p 0.3589386 1.00000000 0.8354038 0.45181397
LR (adj) p 0.2454261 0.83540376 1.0000000 0.34204406
Wilcox p 0.5355871 0.45181397 0.3420441 1.00000000
Maaslin p 0.7721082 0.29158496 0.1887770 0.33639405
Maaslin (adj) p 0.3734800 0.09230949 0.1455309 0.23561082
RF rank 0.1449981 0.15605324 0.1282026 0.03321798
Inv. abs. maaslin coef. (adj) 0.1834648 0.10592778 0.1210874 0.07229872
Inv. abs. GMR-1 0.4358268 0.48933930 0.4050390 0.87975704
Maaslin p Maaslin (adj) p RF rank
Spearman p 0.7721082 0.37347996 0.14499810
LR p 0.2915850 0.09230949 0.15605324
LR (adj) p 0.1887770 0.14553089 0.12820258
Wilcox p 0.3363940 0.23561082 0.03321798
Maaslin p 1.0000000 0.43010166 0.12058106
Maaslin (adj) p 0.4301017 1.00000000 0.04274972
RF rank 0.1205811 0.04274972 1.00000000
Inv. abs. maaslin coef. (adj) 0.2235514 0.74760336 0.14660318
Inv. abs. GMR-1 0.2951789 0.12010106 0.06795601
Inv. abs. maaslin coef. (adj) Inv. abs. GMR-1
Spearman p 0.18346477 0.43582677
LR p 0.10592778 0.48933930
LR (adj) p 0.12108740 0.40503896
Wilcox p 0.07229872 0.87975704
Maaslin p 0.22355141 0.29517889
Maaslin (adj) p 0.74760336 0.12010106
RF rank 0.14660318 0.06795601
Inv. abs. maaslin coef. (adj) 1.00000000 0.03047700
Inv. abs. GMR-1 0.03047700 1.00000000
N features with full data across tests: 1172
Spearman’s rho matrix of statistical test p values - India (neo-)
#### Rho values
Spearman p LR p LR (adj) p Wilcox p
Spearman p 1.00000000 0.01563546 -0.1030347 0.5178582
LR p 0.01563546 1.00000000 0.9288214 0.4880608
LR (adj) p -0.10303473 0.92882139 1.0000000 0.3814178
Wilcox p 0.51785818 0.48806081 0.3814178 1.0000000
Maaslin p 0.60809655 0.19741516 0.1248711 0.3090118
Maaslin (adj) p 0.48763501 0.30055755 0.2787380 0.3401133
RF rank 0.12770066 0.13578743 0.1241735 0.1310259
Inv. abs. maaslin coef. (adj) 0.12013819 0.39673516 0.4534598 0.2110846
Inv. abs. GMR-1 0.32542755 0.62176701 0.5485322 0.8494499
Maaslin p Maaslin (adj) p RF rank
Spearman p 0.6080966 0.4876350 0.1277007
LR p 0.1974152 0.3005576 0.1357874
LR (adj) p 0.1248711 0.2787380 0.1241735
Wilcox p 0.3090118 0.3401133 0.1310259
Maaslin p 1.0000000 0.8292037 0.1604228
Maaslin (adj) p 0.8292037 1.0000000 0.1686369
RF rank 0.1604228 0.1686369 1.0000000
Inv. abs. maaslin coef. (adj) 0.4728154 0.6961492 0.1446916
Inv. abs. GMR-1 0.3151259 0.3678076 0.1374517
Inv. abs. maaslin coef. (adj) Inv. abs. GMR-1
Spearman p 0.1201382 0.3254275
LR p 0.3967352 0.6217670
LR (adj) p 0.4534598 0.5485322
Wilcox p 0.2110846 0.8494499
Maaslin p 0.4728154 0.3151259
Maaslin (adj) p 0.6961492 0.3678076
RF rank 0.1446916 0.1374517
Inv. abs. maaslin coef. (adj) 1.0000000 0.3180210
Inv. abs. GMR-1 0.3180210 1.0000000
N features with full data across tests: 1274
Spearman’s rho matrix of statistical test p values - Malawi
#### Rho values
Spearman p LR p LR (adj) p Wilcox p
Spearman p 1.0000000 0.21040352 0.20376801 0.6462995
LR p 0.2104035 1.00000000 0.74364144 0.3989728
LR (adj) p 0.2037680 0.74364144 1.00000000 0.5056574
Wilcox p 0.6462995 0.39897283 0.50565738 1.0000000
Maaslin p 0.5008018 0.20626761 0.10200900 0.2533428
Maaslin (adj) p 0.4838965 0.20153990 0.10379929 0.2187444
RF rank 0.1430662 0.02554006 0.05013679 0.1070352
Inv. abs. maaslin coef. (adj) 0.3864372 0.08589081 0.13314886 0.1961871
Inv. abs. GMR-1 0.3999077 0.44911485 0.61390270 0.7537418
Maaslin p Maaslin (adj) p RF rank
Spearman p 0.50080181 0.4838965 0.14306624
LR p 0.20626761 0.2015399 0.02554006
LR (adj) p 0.10200900 0.1037993 0.05013679
Wilcox p 0.25334285 0.2187444 0.10703517
Maaslin p 1.00000000 0.9253483 0.07280972
Maaslin (adj) p 0.92534833 1.0000000 0.06055990
RF rank 0.07280972 0.0605599 1.00000000
Inv. abs. maaslin coef. (adj) 0.64832507 0.7287147 0.03891789
Inv. abs. GMR-1 0.16177586 0.1510543 0.10626730
Inv. abs. maaslin coef. (adj) Inv. abs. GMR-1
Spearman p 0.38643724 0.3999077
LR p 0.08589081 0.4491148
LR (adj) p 0.13314886 0.6139027
Wilcox p 0.19618708 0.7537418
Maaslin p 0.64832507 0.1617759
Maaslin (adj) p 0.72871471 0.1510543
RF rank 0.03891789 0.1062673
Inv. abs. maaslin coef. (adj) 1.00000000 0.1646486
Inv. abs. GMR-1 0.16464856 1.0000000
N features with full data across tests: 1247
Dose 1 shedding
Summary plot
Differential features - FDR p <0.2
country n_tested_fisher n_signif_fisher n_tested_lr n_signif_lr
1 MLW 1275 0 1275 0
2 IND (neo-) 1389 0 1389 2
3 IND (neo+) 1211 0 1211 0
4 IND 1360 0 1360 0
n_tested_maaslin n_signif_maaslin
1 2003 0
2 1989 0
3 1985 0
4 2003 0
Summary of prevalence difference distribution
Proportion of features more prevalent in non-responders vs responders
country n_neg n_equal n_pos total proportion_neg
1 IND 828 13 519 1360 60.9%
2 IND (neo+) 521 2 688 1211 43%
3 IND (neo-) 800 10 579 1389 57.6%
4 MLW 830 0 445 1275 65.1%n = prevalence difference <0 (vs >=0).
P values (Wilcoxon test, mean of difference distribution = 0)
[,1]
IND 8.381282e-23
MLW 1.501304e-31
IND_exposed 3.826945e-09
IND_nonexposed 3.497789e-16Summary of adundance difference distribution
P values (Wilcoxon test, mean of difference distribution = 0)
[,1]
IND 2.420885e-40
MLW 9.401433e-18
IND_exposed 1.412866e-31
IND_nonexposed 2.656579e-02Proportion of features more abundant in non-responders vs responders
country n_neg n_equal n_pos total proportion_neg
1 IND 1265 0 738 2003 63.2%
2 IND (neo+) 1199 0 786 1985 60.4%
3 IND (neo-) 1012 0 977 1989 50.9%
4 MLW 871 0 1132 2003 43.5%Summary of MaAsLin2 associations
subset N_features FDR p<0.2 unadjusted FDR p<0.2 adjusted
1 IND 2003 (738 +/1265 -) 0 (0 +/0 -) 0 (0 +/0 -)
2 IND (neo+) 1985 (786 +/1199 -) 0 (0 +/0 -) 0 (0 +/0 -)
3 IND (neo-) 1989 (977 +/1012 -) 0 (0 +/0 -) 0 (0 +/0 -)
4 MLW 2003 (1132 +/871 -) 0 (0 +/0 -) 0 (0 +/0 -)Spearman’s rho matrix of statistical test p values - India
#### Rho values
Fisher p LR p LR (adj) p Wilcox p
Fisher p 1.00000000 0.97450064 0.94075747 0.55994145
LR p 0.97450064 1.00000000 0.96184404 0.55909078
LR (adj) p 0.94075747 0.96184404 1.00000000 0.52432784
Wilcox p 0.55994145 0.55909078 0.52432784 1.00000000
Maaslin p 0.24421798 0.24414193 0.22719764 0.64139933
Maaslin (adj) p 0.25905787 0.25965139 0.26061148 0.61125170
RF rank 0.14295953 0.12875453 0.13746825 0.03373467
Inv. abs. Maaslin coef. (adj) 0.13479778 0.12520365 0.14537506 0.40264970
Inv. abs. prev. diff. 0.92257285 0.93145065 0.89607445 0.53124441
Inv. abs. mean abund. diff. -0.05681511 -0.05758762 -0.04547294 0.03557677
Maaslin p Maaslin (adj) p RF rank
Fisher p 0.24421798 0.25905787 0.14295953
LR p 0.24414193 0.25965139 0.12875453
LR (adj) p 0.22719764 0.26061148 0.13746825
Wilcox p 0.64139933 0.61125170 0.03373467
Maaslin p 1.00000000 0.90268393 0.02613961
Maaslin (adj) p 0.90268393 1.00000000 0.07304124
RF rank 0.02613961 0.07304124 1.00000000
Inv. abs. Maaslin coef. (adj) 0.62738593 0.65885095 0.33703098
Inv. abs. prev. diff. 0.22470699 0.28054594 0.21621596
Inv. abs. mean abund. diff. 0.20892657 0.05306182 0.21164463
Inv. abs. Maaslin coef. (adj)
Fisher p 0.1347978
LR p 0.1252037
LR (adj) p 0.1453751
Wilcox p 0.4026497
Maaslin p 0.6273859
Maaslin (adj) p 0.6588510
RF rank 0.3370310
Inv. abs. Maaslin coef. (adj) 1.0000000
Inv. abs. prev. diff. 0.1241561
Inv. abs. mean abund. diff. 0.6312257
Inv. abs. prev. diff. Inv. abs. mean abund. diff.
Fisher p 0.9225728 -0.05681511
LR p 0.9314507 -0.05758762
LR (adj) p 0.8960745 -0.04547294
Wilcox p 0.5312444 0.03557677
Maaslin p 0.2247070 0.20892657
Maaslin (adj) p 0.2805459 0.05306182
RF rank 0.2162160 0.21164463
Inv. abs. Maaslin coef. (adj) 0.1241561 0.63122567
Inv. abs. prev. diff. 1.0000000 -0.13464200
Inv. abs. mean abund. diff. -0.1346420 1.00000000
N features with full data across tests: 1360
Spearman’s rho matrix of statistical test p values - India (neo+)
#### Rho values
Fisher p LR p LR (adj) p Wilcox p
Fisher p 1.000000000 0.745404031 0.67976763 0.45888266
LR p 0.745404031 1.000000000 0.84909441 0.36358529
LR (adj) p 0.679767631 0.849094413 1.00000000 0.31050842
Wilcox p 0.458882659 0.363585294 0.31050842 1.00000000
Maaslin p 0.146135196 0.072788612 0.05037538 0.70337875
Maaslin (adj) p 0.196879055 0.140930590 0.17034107 0.54112167
RF rank 0.041170759 0.065777059 0.03959159 0.02514755
Inv. abs. Maaslin coef. (adj) 0.002949794 0.006895684 0.05237194 0.37872125
Inv. abs. prev. diff. 0.871151194 0.820753682 0.68113464 0.37291408
Inv. abs. mean abund. diff. -0.165054616 -0.140549039 -0.13503344 0.11928495
Maaslin p Maaslin (adj) p RF rank
Fisher p 0.14613520 0.196879055 0.04117076
LR p 0.07278861 0.140930590 0.06577706
LR (adj) p 0.05037538 0.170341068 0.03959159
Wilcox p 0.70337875 0.541121669 0.02514755
Maaslin p 1.00000000 0.704442218 0.01913084
Maaslin (adj) p 0.70444222 1.000000000 0.07835470
RF rank 0.01913084 0.078354698 1.00000000
Inv. abs. Maaslin coef. (adj) 0.49132676 0.646839354 0.39212367
Inv. abs. prev. diff. 0.07143828 0.212105453 0.11395157
Inv. abs. mean abund. diff. 0.33136678 0.001107176 0.31617122
Inv. abs. Maaslin coef. (adj)
Fisher p 0.002949794
LR p 0.006895684
LR (adj) p 0.052371935
Wilcox p 0.378721250
Maaslin p 0.491326756
Maaslin (adj) p 0.646839354
RF rank 0.392123674
Inv. abs. Maaslin coef. (adj) 1.000000000
Inv. abs. prev. diff. -0.012652994
Inv. abs. mean abund. diff. 0.578479290
Inv. abs. prev. diff. Inv. abs. mean abund. diff.
Fisher p 0.87115119 -0.165054616
LR p 0.82075368 -0.140549039
LR (adj) p 0.68113464 -0.135033443
Wilcox p 0.37291408 0.119284954
Maaslin p 0.07143828 0.331366777
Maaslin (adj) p 0.21210545 0.001107176
RF rank 0.11395157 0.316171218
Inv. abs. Maaslin coef. (adj) -0.01265299 0.578479290
Inv. abs. prev. diff. 1.00000000 -0.246422254
Inv. abs. mean abund. diff. -0.24642225 1.000000000
N features with full data across tests: 1211
Spearman’s rho matrix of statistical test p values - India (neo-)
#### Rho values
Fisher p LR p LR (adj) p Wilcox p
Fisher p 1.00000000 0.91686976 0.8502686 0.5254047
LR p 0.91686976 1.00000000 0.9143489 0.4927810
LR (adj) p 0.85026861 0.91434890 1.0000000 0.4554419
Wilcox p 0.52540469 0.49278100 0.4554419 1.0000000
Maaslin p 0.24313538 0.20259893 0.1922020 0.7066388
Maaslin (adj) p 0.21417833 0.17464944 0.1765315 0.6520412
RF rank 0.33086199 0.31640417 0.3383616 0.2486763
Inv. abs. Maaslin coef. (adj) 0.13932381 0.13299303 0.1443060 0.4319432
Inv. abs. prev. diff. 0.93220784 0.90980214 0.8243270 0.5497942
Inv. abs. mean abund. diff. 0.07462958 0.08436932 0.1094270 0.1037652
Maaslin p Maaslin (adj) p RF rank
Fisher p 0.2431354 0.2141783 0.3308620
LR p 0.2025989 0.1746494 0.3164042
LR (adj) p 0.1922020 0.1765315 0.3383616
Wilcox p 0.7066388 0.6520412 0.2486763
Maaslin p 1.0000000 0.9305087 0.1497336
Maaslin (adj) p 0.9305087 1.0000000 0.1300834
RF rank 0.1497336 0.1300834 1.0000000
Inv. abs. Maaslin coef. (adj) 0.6081066 0.6581822 0.3439254
Inv. abs. prev. diff. 0.2693780 0.2386069 0.3530790
Inv. abs. mean abund. diff. 0.2019029 0.1540531 0.3508385
Inv. abs. Maaslin coef. (adj)
Fisher p 0.1393238
LR p 0.1329930
LR (adj) p 0.1443060
Wilcox p 0.4319432
Maaslin p 0.6081066
Maaslin (adj) p 0.6581822
RF rank 0.3439254
Inv. abs. Maaslin coef. (adj) 1.0000000
Inv. abs. prev. diff. 0.1314581
Inv. abs. mean abund. diff. 0.6939288
Inv. abs. prev. diff. Inv. abs. mean abund. diff.
Fisher p 0.93220784 0.07462958
LR p 0.90980214 0.08436932
LR (adj) p 0.82432696 0.10942697
Wilcox p 0.54979422 0.10376520
Maaslin p 0.26937803 0.20190290
Maaslin (adj) p 0.23860686 0.15405308
RF rank 0.35307904 0.35083845
Inv. abs. Maaslin coef. (adj) 0.13145813 0.69392884
Inv. abs. prev. diff. 1.00000000 0.01651858
Inv. abs. mean abund. diff. 0.01651858 1.00000000
N features with full data across tests: 1389
Spearman’s rho matrix of statistical test p values - Malawi
#### Rho values
Fisher p LR p LR (adj) p Wilcox p
Fisher p 1.00000000 0.54708392 0.39678899 0.4714054
LR p 0.54708392 1.00000000 0.82126153 0.2667955
LR (adj) p 0.39678899 0.82126153 1.00000000 0.2420892
Wilcox p 0.47140542 0.26679549 0.24208918 1.0000000
Maaslin p 0.26373149 0.10898569 0.12186814 0.7636248
Maaslin (adj) p 0.23372452 0.11666025 0.16916951 0.5723617
RF rank 0.11782933 0.21279323 0.20196150 0.1915279
Inv. abs. Maaslin coef. (adj) 0.13031173 0.15557931 0.16903079 0.3567603
Inv. abs. prev. diff. 0.93399338 0.68155934 0.52495128 0.4776807
Inv. abs. mean abund. diff. 0.03568437 0.04908943 0.02236044 0.1543612
Maaslin p Maaslin (adj) p RF rank
Fisher p 0.2637315 0.2337245 0.1178293
LR p 0.1089857 0.1166602 0.2127932
LR (adj) p 0.1218681 0.1691695 0.2019615
Wilcox p 0.7636248 0.5723617 0.1915279
Maaslin p 1.0000000 0.7985001 0.1993738
Maaslin (adj) p 0.7985001 1.0000000 0.1960889
RF rank 0.1993738 0.1960889 1.0000000
Inv. abs. Maaslin coef. (adj) 0.5275515 0.6834767 0.5189899
Inv. abs. prev. diff. 0.2766448 0.2615907 0.1699692
Inv. abs. mean abund. diff. 0.2887579 0.1857796 0.4872037
Inv. abs. Maaslin coef. (adj)
Fisher p 0.1303117
LR p 0.1555793
LR (adj) p 0.1690308
Wilcox p 0.3567603
Maaslin p 0.5275515
Maaslin (adj) p 0.6834767
RF rank 0.5189899
Inv. abs. Maaslin coef. (adj) 1.0000000
Inv. abs. prev. diff. 0.1651108
Inv. abs. mean abund. diff. 0.7272972
Inv. abs. prev. diff. Inv. abs. mean abund. diff.
Fisher p 0.9339934 0.03568437
LR p 0.6815593 0.04908943
LR (adj) p 0.5249513 0.02236044
Wilcox p 0.4776807 0.15436123
Maaslin p 0.2766448 0.28875795
Maaslin (adj) p 0.2615907 0.18577961
RF rank 0.1699692 0.48720368
Inv. abs. Maaslin coef. (adj) 0.1651108 0.72729720
Inv. abs. prev. diff. 1.0000000 0.02884730
Inv. abs. mean abund. diff. 0.0288473 1.00000000
N features with full data across tests: 1275
Summary plots
Seroconversion
IgA
Dose 1 shedding
Session info
R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur ... 10.16
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] Maaslin2_1.10.0 FSA_0.9.3 ALDEx2_1.28.1
[4] zCompositions_1.4.0-1 truncnorm_1.0-8 NADA_1.6-1.1
[7] survival_3.4-0 MASS_7.3-58.1 sjstats_0.18.1
[10] ggExtra_0.10.0 formattable_0.2.1 inlmisc_0.5.5
[13] wesanderson_0.3.6 phangorn_2.10.0 ape_5.6-2
[16] DECIPHER_2.24.0 RSQLite_2.2.18 Biostrings_2.64.1
[19] GenomeInfoDb_1.32.4 XVector_0.36.0 IRanges_2.30.1
[22] S4Vectors_0.34.0 BiocGenerics_0.42.0 cowplot_1.1.1
[25] scales_1.2.1 RVAideMemoire_0.9-81-2 DescTools_0.99.47
[28] ggsignif_0.6.4 binom_1.1-1.1 shiny_1.7.3
[31] randomcoloR_1.1.0.1 crossval_1.0.4 labdsv_2.0-1
[34] mgcv_1.8-41 nlme_3.1-160 ggpubr_0.4.0
[37] data.table_1.14.4 corrplot_0.92 vegan_2.6-4
[40] lattice_0.20-45 permute_0.9-7 randomForest_4.7-1.1
[43] matrixStats_0.62.0 lme4_1.1-30 Matrix_1.5-1
[46] reshape2_1.4.4 pheatmap_1.0.12 DT_0.26
[49] plotly_4.10.0 cluster_2.1.4 tidyr_1.2.1
[52] dplyr_1.0.10 magrittr_2.0.3 plyr_1.8.7
[55] kableExtra_1.3.4 gridExtra_2.3 RColorBrewer_1.1-3
[58] knitr_1.40 ggplot2_3.3.6 phyloseq_1.40.0
loaded via a namespace (and not attached):
[1] estimability_1.4.1 coda_0.19-4
[3] bit64_4.0.5 DelayedArray_0.22.0
[5] RCurl_1.98-1.9 generics_0.1.3
[7] terra_1.6-17 proxy_0.4-27
[9] bit_4.0.4 webshot_0.5.4
[11] xml2_1.3.3 httpuv_1.6.6
[13] SummarizedExperiment_1.26.1 assertthat_0.2.1
[15] xfun_0.34 jquerylib_0.1.4
[17] evaluate_0.17 promises_1.2.0.1
[19] DEoptimR_1.0-11 fansi_1.0.3
[21] readxl_1.4.1 igraph_1.3.5
[23] DBI_1.1.3 htmlwidgets_1.5.4
[25] purrr_0.3.5 ellipsis_0.3.2
[27] backports_1.4.1 V8_4.2.1
[29] insight_0.18.6 MatrixGenerics_1.8.1
[31] vctrs_0.5.0 Biobase_2.56.0
[33] sjlabelled_1.2.0 abind_1.4-5
[35] cachem_1.0.6 withr_2.5.0
[37] robustbase_0.95-0 rgdal_1.5-32
[39] emmeans_1.8.2 getopt_1.20.3
[41] svglite_2.1.0 lazyeval_0.2.2
[43] crayon_1.5.2 flexdashboard_0.6.0
[45] pkgconfig_2.0.3 labeling_0.4.2
[47] rlang_1.0.6 lifecycle_1.0.3
[49] miniUI_0.1.1.1 modelr_0.1.9
[51] cellranger_1.1.0 datawizard_0.6.3
[53] raster_3.6-3 carData_3.0-5
[55] lpsymphony_1.24.0 Rhdf5lib_1.18.2
[57] boot_1.3-28 viridisLite_0.4.1
[59] parameters_0.19.0 rootSolve_1.8.2.3
[61] bitops_1.0-7 rhdf5filters_1.8.0
[63] blob_1.2.3 stringr_1.4.1
[65] rstatix_0.7.0 memoise_2.0.1
[67] zlibbioc_1.42.0 compiler_4.2.1
[69] cli_3.4.1 ade4_1.7-19
[71] tidyselect_1.2.0 stringi_1.7.8
[73] highr_0.9 yaml_2.3.6
[75] grid_4.2.1 sass_0.4.2
[77] fastmatch_1.1-3 tools_4.2.1
[79] lmom_2.9 rstudioapi_0.14
[81] foreach_1.5.2 optparse_1.7.3
[83] gld_2.6.6 farver_2.1.1
[85] Rtsne_0.16 RcppZiggurat_0.1.6
[87] digest_0.6.30 quadprog_1.5-8
[89] Rcpp_1.0.9 GenomicRanges_1.48.0
[91] car_3.1-1 broom_1.0.1
[93] performance_0.10.0 later_1.3.0
[95] httr_1.4.4 effectsize_0.8.1
[97] colorspace_2.0-3 rvest_1.0.3
[99] splines_4.2.1 expm_0.999-6
[101] sp_1.5-0 multtest_2.52.0
[103] Exact_3.2 systemfonts_1.0.4
[105] xtable_1.8-4 jsonlite_1.8.3
[107] nloptr_2.0.3 Rfast_2.0.6
[109] R6_2.5.1 pillar_1.8.1
[111] htmltools_0.5.3 mime_0.12
[113] glue_1.6.2 fastmap_1.1.0
[115] minqa_1.2.5 BiocParallel_1.30.4
[117] class_7.3-20 codetools_0.2-18
[119] pcaPP_2.0-3 mvtnorm_1.1-3
[121] utf8_1.2.2 bslib_0.4.0
[123] tibble_3.1.8 curl_4.3.3
[125] biglm_0.9-2.1 rmarkdown_2.17
[127] biomformat_1.24.0 munsell_0.5.0
[129] e1071_1.7-12 rhdf5_2.40.0
[131] GenomeInfoDbData_1.2.8 iterators_1.0.14
[133] sjmisc_2.8.9 gtable_0.3.1
[135] bayestestR_0.13.0 .